Season 1: Lincoln Burrows is on death row for the murder of the Vice President's brother. He insists he's innocent, but no one other than his brother Michael Scofield believes him. An engineer who was hired to renovate the prison where Lincoln is being held, Michael takes drastic measures to help his brother. He robs a bank and is sent to the same prison, so that with his knowledge of the building the two of them can escape together. Michael also discovers a massive governmental conspiracy that is determined to see Lincoln executed when two crooked federal agents try to silence Burrows' ex-wife and son.

Season 2: Now on the run, Michael and Lincoln work at unraveling the conspiracy that put them in this situation in the first place. Pursued by FBI agent Alexander Mahone, who has been ordered by "The Company" to leave no one alive, the duo face insurmountable odds in their quest to bring justice to the conspiracy responsible for so many deaths.

Season 3: Having made it to Panama, Michael finds himself incarcerated in a very different kind of prison. "The Company" delivers an ultimatum: break out fellow inmate James Whistler, or they will kill Sara Tancredi and LJ Burrows.